scholarly journals Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 601 ◽  
Author(s):  
Johanna Nelkner ◽  
Gonzalo Torres Tejerizo ◽  
Julia Hassa ◽  
Timo Wentong Lin ◽  
Julian Witte ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Genome Mining ◽  
Gene Clusters ◽  
Disease Suppression ◽  
Biocontrol Agents ◽  
Circular Chromosome ◽  
Pseudomonas Brassicacearum

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

scholarly journals Perception of Biocontrol Potential of Bacillusinaquosorum KR2-7 against Tomato Fusarium Wilt through Merging Genome Mining with Chemical Analysis

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 137
Author(s):  
Maedeh Kamali ◽  
Dianjing Guo ◽  
Shahram Naeimi ◽  
Jafar Ahmadi
Keyword(s):  
Chemical Analysis ◽  
Plant Growth ◽  
Fusarium Wilt ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Genome Mining ◽  
Gene Clusters ◽  
Systemic Resistance ◽  
Plant Colonization ◽  
Biocontrol Potential

Tomato Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), is a destructive disease that threatens the agricultural production of tomatoes. In the present study, the biocontrol potential of strain KR2-7 against Fol was investigated through integrated genome mining and chemical analysis. Strain KR2-7 was identified as B. inaquosorum based on phylogenetic analysis. Through the genome mining of strain KR2-7, we identified nine antifungal and antibacterial compound biosynthetic gene clusters (BGCs) including fengycin, surfactin and Bacillomycin F, bacillaene, macrolactin, sporulation killing factor (skf), subtilosin A, bacilysin, and bacillibactin. The corresponding compounds were confirmed through MALDI-TOF-MS chemical analysis. The gene/gene clusters involved in plant colonization, plant growth promotion, and induced systemic resistance were also identified in the KR2-7 genome, and their related secondary metabolites were detected. In light of these results, the biocontrol potential of strain KR2-7 against tomato Fusarium wilt was identified. This study highlights the potential to use strain KR2-7 as a plant-growth promotion agent.

scholarly journals Genome Mining of Antimicrobial Gene Clusters from Phyllospheric Bacteria Isolated from Solanum Lycopersicum and Lactuca Sativa to Identify Biocontrol Properties

2021 ◽  
Author(s):  
Claudia Y. Muñoz ◽  
Lu Zhou ◽  
Yunhai Yi ◽  
Oscar P. Kuipers
Keyword(s):  
Antimicrobial Activity ◽  
Plant Growth ◽  
Plant Pathogens ◽  
Growth Promotion ◽  
Genome Mining ◽  
Gene Clusters ◽  
Biocontrol Agents ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Microbe Interactions

Abstract BackgroundBiocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyllosphere microbiology is of vital importance for biocontrol development. Most studies have been directed towards beneficial plant-microbe interactions and ignore the pathogens that might affect humans when consuming vegetables. In this study we extended this perspective and investigated potential biocontrol strains isolated from the tomato and lettuce phyllosphere that can promote plant growth and antagonize mammalian pathogens as well as plant pathogens. Subsequently, we mined into their genomes for discovery of antimicrobial biosynthetic gene clusters (BGCs), several of which are good candidates to produce protectants against microbial plant and mammalian pathogens.Results The antimicrobial activity of 69 newly isolated strains from a healthy tomato and lettuce phyllosphere against several plant and mammalian pathogens was determined with plates assays. Three strains with the highest antimicrobial activity against the relevant pathogens were selected and characterized (Bacillus subtilis STRP31, Bacillus velezensis SPL51, and Paenibacillus sp. PL91). All three strains showed a plant growth promotion effect by the production of volatile compounds (VOCs) on tomato and lettuce. In addition, genome mining of these isolates showed the presence of a large variety of biosynthetic gene clusters. A total of 39 BGCs were identified, of which several are already known, such as bacilysin, bacillibactin, surfactin, subtilomycin, etc., but also several novel ones. Further analysis revealed that among the novel BGCs, one NRPS and two bacteriocins are encoded which were analyzed in more depth.Conclusions Several antimicrobial BGCs were found in the selected strains, including the rediscovery of known ones, but also the discovery of novel ones. Our study serves as support for subsequent examination and characterization of novel antimicrobial metabolites, and the possibility of developing biocontrol agents.

scholarly journals Genome Mining and Evaluation of the Biocontrol Potential of Pseudomonas fluorescens BRZ63, a New Endophyte of Oilseed Rape (Brassica napus L.) against Fungal Pathogens

2020 ◽  
Vol 21 (22) ◽  
pp. 8740
Author(s):  
Daria Chlebek ◽  
Artur Pinski ◽  
Joanna Żur ◽  
Justyna Michalska ◽  
Katarzyna Hupert-Kocurek
Keyword(s):  
Brassica Napus ◽  
Plant Growth ◽  
Pseudomonas Fluorescens ◽  
Oilseed Rape ◽  
Plant Growth Promotion ◽  
Fungal Pathogens ◽  
Growth Promotion ◽  
Genome Mining ◽  
Plant Colonization ◽  
Brassica Napus L

Endophytic bacteria hold tremendous potential for use as biocontrol agents. Our study aimed to investigate the biocontrol activity of Pseudomonas fluorescens BRZ63, a new endophyte of oilseed rape (Brassica napus L.) against Rhizoctonia solani W70, Colletotrichum dematium K, Sclerotinia sclerotiorum K2291, and Fusarium avenaceum. In addition, features crucial for biocontrol, plant growth promotion, and colonization were assessed and linked with the genome sequences. The in vitro tests showed that BRZ63 significantly inhibited the mycelium growth of all tested pathogens and stimulated germination and growth of oilseed rape seedlings treated with fungal pathogens. The BRZ63 strain can benefit plants by producing biosurfactants, siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia as well as phosphate solubilization. The abilities of exopolysaccharide production, autoaggregation, and biofilm formation additionally underline its potential to plant colonization and hence biocontrol. The effective colonization properties of the BRZ63 strain were confirmed by microscopy observations of EGFP-expressing cells colonizing the root surface and epidermal cells of Arabidopsis thaliana Col-0. Genome mining identified many genes related to the biocontrol process, such as transporters, siderophores, and other secondary metabolites. All analyses revealed that the BRZ63 strain is an excellent endophytic candidate for biocontrol of various plant pathogens and plant growth promotion.

EFFICACY OF RHIZOBACTERIA ON PLANT GROWTH PROMOTION AND DISEASE SUPPRESSION IN VITRO

2012 ◽  
pp. 525-532 ◽  
Author(s):  
S. Velivelli ◽  
E. O'Herlihy ◽  
B. Janczura ◽  
B. Doyle Prestwich ◽  
J. Ghyselinck ◽  
...  
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Disease Suppression

scholarly journals Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals

2020 ◽  
Vol 8 (2) ◽  
pp. 153 ◽  
Author(s):  
Francesca Luziatelli ◽  
Anna Grazia Ficca ◽  
Mariateresa Cardarelli ◽  
Francesca Melini ◽  
Andrea Cavalieri ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Plant Growth ◽  
Plant Growth Promotion ◽  
Plant Pathogens ◽  
Growth Promotion ◽  
Pantoea Agglomerans ◽  
Toxic Heavy Metals ◽  
Circular Chromosome ◽  
Plant Growth Promoting ◽  
Genetic Mechanisms

Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.

scholarly journals Chitosan for Plant Growth Promotion and Disease Suppression against Anthracnose in Chilli

2018 ◽  
Vol 3 (3) ◽  
pp. 806-817 ◽  
Author(s):  
Jahanara Akter ◽  
Rayhanur Jannat ◽  
Md. Motaher Hossain ◽  
Jalal Uddin Ahmed ◽  
Md. Tanbir Rubayet
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Disease Suppression

Mechanisms of plant growth promotion and disease suppression byPseudomonas aeruginosastrain 2apa

2013 ◽  
Vol 54 (8) ◽  
pp. 792-801 ◽  
Author(s):  
P. Hariprasad ◽  
S. Chandrashekar ◽  
S. Brijesh Singh ◽  
S. R. Niranjana
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Disease Suppression

scholarly journals The Significance of Bacillus spp. in Disease Suppression and Growth Promotion of Field and Vegetable Crops

2020 ◽  
Vol 8 (7) ◽  
pp. 1037 ◽  
Author(s):  
Dragana Miljaković ◽  
Jelena Marinković ◽  
Svetlana Balešević-Tubić
Keyword(s):  
Plant Growth ◽  
Plant Pathogens ◽  
Growth Promotion ◽  
Disease Suppression ◽  
Biocontrol Agents ◽  
Systemic Resistance ◽  
Steady Increase ◽  
Vegetable Crops ◽  
Wide Range ◽  
Bacillus Spp

Bacillus spp. produce a variety of compounds involved in the biocontrol of plant pathogens and promotion of plant growth, which makes them potential candidates for most agricultural and biotechnological applications. Bacilli exhibit antagonistic activity by excreting extracellular metabolites such as antibiotics, cell wall hydrolases, and siderophores. Additionally, Bacillus spp. improve plant response to pathogen attack by triggering induced systemic resistance (ISR). Besides being the most promising biocontrol agents, Bacillus spp. promote plant growth via nitrogen fixation, phosphate solubilization, and phytohormone production. Antagonistic and plant growth-promoting strains of Bacillus spp. might be useful in formulating new preparations. Numerous studies of a wide range of plant species revealed a steady increase in the number of Bacillus spp. identified as potential biocontrol agents and plant growth promoters. Among different mechanisms of action, it remains unclear which individual or combined traits could be used as predictors in the selection of the best strains for crop productivity improvement. Due to numerous factors that influence the successful application of Bacillus spp., it is necessary to understand how different strains function in biological control and plant growth promotion, and distinctly define the factors that contribute to their more efficient use in the field.

scholarly journals Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257863
Author(s):  
Nazia R. Zaman ◽  
Umar F. Chowdhury ◽  
Rifath N. Reza ◽  
Farhana T. Chowdhury ◽  
Mrinmoy Sarker ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Genome Mining ◽  
Gene Clusters ◽  
Macrophomina Phaseolina ◽  
Melanin Synthesis ◽  
Burkholderia Contaminans ◽  
Plant Growth Promoting ◽  
Growth Promoting

The endophytic bacterium Burkholderia contaminans NZ was isolated from jute, which is an important fiber-producing plant. This bacterium exhibits significant growth promotion activity in in vivo pot experiments, and like other plant growth-promoting (PGP) bacteria fixes nitrogen, produces indole acetic acid (IAA), siderophore, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. B. contaminans NZ is considered to exert a promising growth inhibitory effect on Macrophomina phaseolina, a phytopathogen responsible for infecting hundreds of crops worldwide. This study aimed to identify the possibility of B. contaminans NZ as a safe biocontrol agent and assess its effectiveness in suppressing phytopathogenic fungi, especially M. phaseolina. Co-culture of M. phaseolina with B. contaminans NZ on both solid and liquid media revealed appreciable growth suppression of M. phaseolina and its chromogenic aberration in liquid culture. Genome mining of B. contaminans NZ using NaPDoS and antiSMASH revealed gene clusters that displayed 100% similarity for cytotoxic and antifungal substances, such as pyrrolnitrin. GC-MS analysis of B. contaminans NZ culture extracts revealed various bioactive compounds, including catechol; 9,10-dihydro-12’-hydroxy-2’-methyl-5’-(phenylmethyl)- ergotaman 3’,6’,18-trione; 2,3-dihydro-3,5- dihydroxy-6-methyl-4H-pyran-4-one; 1-(1,6-Dioxooctadecyl)- pyrrolidine; 9-Octadecenamide; and 2- methoxy- phenol. These compounds reportedly exhibit tyrosinase inhibitory, antifungal, and antibiotic activities. Using a more targeted approach, an RP-HPLC purified fraction was analyzed by LC-MS, confirming the existence of pyrrolnitrin in the B. contaminans NZ extract. Secondary metabolites, such as catechol and ergotaman, have been predicted to inhibit melanin synthesis in M. phaseolina. Thus, B. contaminans NZ appears to inhibit phytopathogens by apparently impairing melanin synthesis and other potential biochemical pathways, exhibiting considerable fungistatic activity.

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